When nukes are involved things get taken very seriously. Nobody wants to be the guy who thought it would all blow over and got it wrong.
And yeah, I'm sure the western intelligence-agencies are as sure to plant moles in anti-nuclear movements as in the rapidly deteriorating Turkish military high command.
Sorry for the sarcasm, but c'mon.
PS. Moreover, large quantities of mustard agent were found in Syria in 2013.
Agents have historically been fond of generating false intelligence to prove that they are valuable, and historical documentation has shown that agents aren't always that competent.
Using technology certainly helps, but it has its limits. Human intelligence tends to get better information, but can be unreliable and generate lots of false information.
It would not surprise me at all if intelligence agencies failed to realize something is coming. Hindsight shows that the intelligence failures in 9/11 and Iraq were due to valuable information not being identified or the intelligence community sucking up false information from informants who were just making it up to stay in the CIA payroll. It's a real hit and miss sort of business.
If what you write is true they should have had clear warning about that coup attempt. It might have succeeded.
Or, the relevant intelligence agencies had clear warning, a good estimate of capabilities and what it would take to defeat it, and were able to intervene to assure that the Erdogan government was capable of putting down the coup
Or they had clear warning, sufficient intelligence about the intentions and orientation of the coup plotters that they were comfortable that the weapons would be no less safe even if the coup succeeded.
Or...
I would also be surprised if (besides initial instability) the expected outcome of a military coup is much worse than the status quo.
With the current situation there's probably not much good of saying "yeah, that place is pretty fked so we gtfo'd." Which exactly the message sent by loading up all your nukes and gtfoing at ~Mach 2.
Because they correctly perceive there's very little risk in remaining there.